you may need to change the car iphone kit to something similar to this:
Just to let you know that you are not alone, and also, to bump this thread in case something has come up.
I've been reading forums that range from 2008-2012 all dealing with the exact same issue.
A VERY interesting piece of information I came across: When using the app "Viber" for calls, the audio is actually routed through your stereo! This is a quick fix, but for me Viber is not perfectly reliable for voice calls, so I'd like to see a fix for iPhone's native phone app.
However, what it does show is something VERY important: that this is a software issue and a jailbreak tweak would do the trick!